Methods and compositions for determining whether a subject carries a gene mutation associated with hereditary hearing loss

Abstract

Methods are provided for determining whether a subject carries a gene mutation associated with Hereditary Hearing Loss (HHL). In practicing the subject methods, an array comprising a plurality of HHL-associated gene mutation probes is contacted with a nucleic acid sample from the subject, and the presence of any resultant surface bound target nucleic acids is detected to determine whether the subject carries a HHL-associated gene mutation. In addition, reagents and kits thereof that find use in practicing the subject methods are provided.

1 . A method of determining whether a subject carries a HHL (Hereditary Hearing Loss) associated gene mutation, said method comprising: 
 (a) contacting an array comprising a plurality of distinct nucleic acid HHL gene mutation probes immobilized on a surface of a solid support with a nucleic acid sample from said subject to produce a sample contacted array;    (b) contacting said sample contacted array with a polymerase and at least two different distinguishably labeled dideoxynucleotides under primer extension conditions; and    (c) detecting the presence of any resultant terminally labeled nucleic acids immobilized on said substrate surface to determine whether said subject carries a HHL gene mutation.    
   
   
       2 . The method according to  claim 1 , wherein said array comprises at least about 50 gene mutation probes for the mutations listed in Table 1.  
   
   
       3 . The method according to  claim 1 , wherein said nucleic acid sample is an amplified genomic sample.  
   
   
       4 . The method according to  claim 3 , wherein said amplified genomic sample is a fragmented amplified genomic sample.  
   
   
       5 . The method according to  claim 4 , wherein said fragmented amplified genomic sample is an enzymatically fragmented sample.  
   
   
       6 . The method according to  claim 1 , wherein said array comprises a plurality of pairs of HHL gene mutation probes, wherein each pair comprises a sense strand probe and an antisense strand probe.  
   
   
       7 . The method according to  claim 1 , wherein said sample contacted array is contacted with four different distinguishably labeled ddNTPs.  
   
   
       8 . The method according to  claim 7 , wherein said four different distinguishably labeled ddNTPs are ddATP, ddTTP, ddGTP and ddCTP.  
   
   
       9 . The method according to  claim 1 , wherein said at least two dideoxynucleotides are labeled with fluorescent labels.  
   
   
       10 . The method according to  claim 9 , wherein said detecting step comprises scanning said surface for said at least two different fluorescent labels.  
   
   
       11 . The method according to  claim 10 , wherein said surface is scanned for four different fluorescent labels.  
   
   
       12 . The method according to  claim 1 , wherein said method is a method for determining whether said subject is heterozygous for a HHL gene mutation.  
   
   
       13 . The method according to  claim 1 , wherein said method is a method for determining whether said subject is homozygous for a HHL gene mutation.  
   
   
       14 . An array comprising a plurality of at least about 50 distinct nucleic acid HHL gene mutation probes immobilized on a surface of a solid support.  
   
   
       15 . The array according to  claim 14 , wherein said at least about 50 distinct gene mutation probes are for the mutations listed in Table 1.  
   
   
       16 . The array according to  claim 14 , wherein said array comprises a plurality of pairs of HHL gene mutation probes, wherein each pair comprises a sense strand probe and an antisense strand probe.  
   
   
       17 . The array according to  claim 14 , wherein said array comprises at least about 100 distinct nucleic acid HHL gene mutation probes.  
   
   
       18 . The array according to  claim 17 , wherein said array comprises at least about 150 distinct nucleic acid HHL gene mutation probes.  
   
   
       19 . (canceled)  
   
   
       20 . A kit for use determining whether a subject carries a HHL (Hereditary Hearing Loss) associated gene mutation gene mutation, said kit comprising; 
 (a) an array comprising a plurality of at least about 50 distinct nucleic acid HHL gene mutation probes immobilized on a surface of a solid support; and    (b) at least two different distinguishably labeled dideoxynucleotides (ddNTPs).    
   
   
       21 - 26 . (canceled)  
   
   
       27 . A method of determining whether any of a plurality of subjects carry a HHL associated gene mutation, said method comprising: 
 (a) producing a plurality of nucleic acid samples from said plurality of subjects, wherein each of said plurality of nucleic acid samples corresponds to one of said plurality of subjects;    (b) contacting each of said plurality of nucleic acid samples with an array comprising a plurality of distinct nucleic acid HHL gene mutation probes immobilized on a surface of a solid support to produce a plurality of sample contacted arrays;    (c) contacting each of said plurality of sample contacted arrays with a polymerase and at least two different distinguishably labeled dideoxynucleotides under primer extension conditions; and    (d) detecting the presence of any resultant terminally labeled nucleic acids immobilized on said substrate surface to determine whether any of said plurality of subjects carry a HHL gene mutation.    
   
   
       28 . The method according to  claim 27 , wherein the accuracy of said method is about 90% or greater.  
   
   
       29 - 30 . (canceled)